Hi Sean, Thanks for the update. So post release I would be able to run mvn clean install on web rest module rather than relying on resources in .m2 folder you mean? Infact I was trying to build them on a machine which doesnt have any historic jars in the .m2 folder and thats why it was failing. And ytex issue still remains a mystery to me. If you have some time this week, we can connect to understand what exactly is the problem.
On Thu, 2 May 2024 at 02:32, Finan, Sean <sean.fi...@childrens.harvard.edu.invalid> wrote: > Hi Gandhi, > > I can build the web-rest module. I should have mentioned that to build > any of the rest projects you need to run mvn install. As the rest requires > 5.1.0 module jars and they don't exist externally (pre-release), maven must > be able to fetch them from your .m2 directory. > > I haven't been able to duplicate the ytex problems that you see and don't > know what might be causing them. > > Sean > > ________________________________ > From: gandhi rajan <gandhiraja...@gmail.com> > Sent: Tuesday, April 30, 2024 11:18 AM > To: dev@ctakes.apache.org <dev@ctakes.apache.org> > Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate > [EXTERNAL] > > * External Email - Caution * > > > Hi Peter, > > Thanks for the response. I dont think the generate test action is trying to > use mysql but hsql DB. Anyways, I am able to build other modules apart from > ytex and ytex-uima module. > > Sean, did you try building ctakes-web-rest module by any chance? It seems > to be broken in my case. > > On Tue, 30 Apr 2024 at 01:28, Peter Abramowitsch <pabramowit...@gmail.com> > wrote: > > > Hi Gandhi, I think the email from Jeff Painter may explain your > > situation. It's a question of your version of mysql being new. The > > crucial lines in your trace are: > > > > org.apache.ctakes.jdl.AppMain.main(AppMain.java:84) > > [INFO] [java] Caused by: > > java.lang.reflect.InaccessibleObjectException: Unable to make protected > > final java.lang.Class > > java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) throws > > java.lang.ClassFormatError accessible: module java.base does not "opens > > java.lang" to unnamed module @61ca2dfa > > > > And this makes it sound like it is expecting a library version where > > certain classnames or accessibility has changed. Check Jeff's pull > > requests and see if that fixes your problem. > > > > Another quick trick is maven .... -fae (Fail at end) It will go > > through the rest of the build and only show failures then > > Peter > > > > On Mon, Apr 29, 2024 at 12:29 PM gandhi rajan <gandhiraja...@gmail.com> > > wrote: > > > > > HI Peter, > > > > > > Thanks for the insights. I tried to debug from AppMain.java and it > > > eventually fails in > > > > > > > > > "org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBind.<init>(ObjectFactoryBind.java:43)" > > > > > > Attaching the complete stacktrace for reference: > > > > > > > > > [INFO] [java] invoking method > > > [INFO] [java] Exception in thread "main" > > > java.lang.ExceptionInInitializerError > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.reflect.opt.AccessorInjector.prepare(AccessorInjector.java:83) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(OptimizedAccessorFactory.java:176) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.reflect.Accessor$FieldReflection.optimize(Accessor.java:282) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.property.SingleElementNodeProperty.<init>(SingleElementNodeProperty.java:94) > > > [INFO] [java] at > > > > > > > > > java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native > > > Method) > > > [INFO] [java] at > > > > > > > > > java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) > > > [INFO] [java] at > > > > > > > > > java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) > > > [INFO] [java] at > > > > > > > > > java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499) > > > [INFO] [java] at > > > > java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:128) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.<init>(ClassBeanInfoImpl.java:181) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:509) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:326) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:141) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl$JAXBContextBuilder.build(JAXBContextImpl.java:1163) > > > [INFO] [java] at > > > > com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:145) > > > [INFO] [java] at > > > > com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:236) > > > [INFO] [java] at > > > java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native > > > Method) > > > [INFO] [java] at > > > > > > > > > java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) > > > [INFO] [java] at > > > > > > > > > java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > > > [INFO] [java] at > > > java.base/java.lang.reflect.Method.invoke(Method.java:568) > > > [INFO] [java] at > > > javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:171) > > > [INFO] [java] at > > > javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:129) > > > [INFO] [java] at > > > javax.xml.bind.ContextFinder.find(ContextFinder.java:307) > > > [INFO] [java] at > > > javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:478) > > > [INFO] [java] at > > > javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:435) > > > [INFO] [java] at > > > javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:336) > > > [INFO] [java] at > > > > > > > > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBind.<init>(ObjectFactoryBind.java:43) > > > [INFO] [java] at > > > > > > > > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getObjectFactoryMapping(ObjectFactoryUtil.java:41) > > > [INFO] [java] at > > > > > > > > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getJAXBElementBySrcXml(ObjectFactoryUtil.java:49) > > > [INFO] [java] at > > > > > > > > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getConnTypeBySrcXml(ObjectFactoryUtil.java:86) > > > [INFO] [java] at > > > > > > > > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getJdbcTypeBySrcXml(ObjectFactoryUtil.java:64) > > > [INFO] [java] at > > > org.apache.ctakes.jdl.AppJdl.execute(AppJdl.java:80) > > > [INFO] [java] at > > > org.apache.ctakes.jdl.AppMain.main(AppMain.java:84) > > > [INFO] [java] Caused by: > > > java.lang.reflect.InaccessibleObjectException: Unable to make protected > > > final java.lang.Class > > > java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) > throws > > > java.lang.ClassFormatError accessible: module java.base does not "opens > > > java.lang" to unnamed module @61ca2dfa > > > [INFO] [java] at > > > > > > > > > java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354) > > > [INFO] [java] at > > > > > > > > > java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297) > > > [INFO] [java] at > > > > java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:199) > > > [INFO] [java] at > > > java.base/java.lang.reflect.Method.setAccessible(Method.java:193) > > > [INFO] [java] at > > > > com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:177) > > > [INFO] [java] at > > > > com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:172) > > > [INFO] [java] at > > > > > > > > > java.base/java.security.AccessController.doPrivileged(AccessController.java:318) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.reflect.opt.Injector.<clinit>(Injector.java:172) > > > [INFO] [java] ... 34 more > > > > > > On Mon, 29 Apr 2024 at 21:21, Peter Abramowitsch < > > pabramowit...@gmail.com> > > > wrote: > > > > > > > I think this is the class where Java is exiting with 1 > > > > /ctakes-ytex/src/test/java/org/apache/ctakes/jdl/AppMainTest.java > > > > > > > > btw my environment is MacOS and I notice yours is Windows, so the > root > > > > cause why this class is giving you trouble is something I wouldn't be > > > able > > > > to help you with. But some debug statements rather than asserts > would > > > tell > > > > you, I think. > > > > > > > > Peter > > > > > > > > On Mon, Apr 29, 2024 at 8:43 AM Peter Abramowitsch < > > > > pabramowit...@gmail.com> > > > > wrote: > > > > > > > > > Hi Gandhi > > > > > This project is an odd one in the sense that when you tell it to > skip > > > the > > > > > tests, it still goes through the effort in building up the db > > > environment > > > > > that the tests would use. But in any case, for me it does build > > either > > > > > way. In the attached log, I've run a maven clean before doing the > > > build > > > > > without tests. > > > > > > > > > > However, check my previous email about your issue. Whereas you'd > > > > narrowed > > > > > it down to a script, I found a line in your email which showed the > > > error > > > > > within that script's execution: A java program: jdl running as > > > App.Main > > > > > threw an assertion on one of the tasks connected with the mysql > > > database > > > > it > > > > > was trying to configure. You could put some debugging statements > in > > > > there > > > > > to see which one. > > > > > > > > > > Peter > > > > > > > > > > On Mon, Apr 29, 2024 at 4:55 AM gandhi rajan < > > gandhiraja...@gmail.com> > > > > > wrote: > > > > > > > > > >> Thanks for the insights Peter. I dint make it clear that I did ran > > the > > > > >> install on ytex module with test case execution toggled off. I > used > > > the > > > > >> following command - "mvn -e clean install -Dmaven.test.skip=true" > > and > > > I > > > > >> still hit the same error. > > > > >> > > > > >> On digging deep, I could find that the build process is trying to > > > > execute > > > > >> "<ant antfile="build-setup.xml" dir="scripts" > target="test.setup">" > > in > > > > >> build-main.xml which in turn is trying to invoke the following > > target > > > in > > > > >> build.setup.xml: > > > > >> > > > > >> <target name="test.setup" description="setup properties and > database > > > for > > > > >> unit tests" > > > > >> > depends="generateTestYtexProperties,templateToConfig,deleteTestDb"> > > > > >> <ant dir="data" target="all" inheritAll="true"/> > > > > >> </target> > > > > >> > > > > >> Did you try running this on a fresh setup Peter? > > > > >> > > > > >> On Sun, 28 Apr 2024 at 01:17, Peter Abramowitsch < > > > > pabramowit...@gmail.com > > > > >> > > > > > >> wrote: > > > > >> > > > > >> > Hi Gandhi > > > > >> > Your error appears to be at this line > > > > >> > > > > > >> > > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: > > > > >> Java > > > > >> > returned: 1 > > > > >> > > > > > >> > A test application being run here: AppMain is in charge of > > loading > > > a > > > > >> > temporary mysqldb that is used to test that part of ytex. For > me > > > it > > > > is > > > > >> > working, but if you can find a way to run that surefire test in > > the > > > > >> > debugger, you can find out why it's failing on one of the > > > assertions. > > > > >> > Otherwise you can take this shortcut > > > > >> > > > > > >> > mvn <goal> -Dmaven.test.skip=true > > > > >> > > > > > >> > To build the project without running any tests. > > > > >> > > > > > >> > On Sat, Apr 27, 2024 at 7:35 AM gandhi rajan < > > > gandhiraja...@gmail.com > > > > > > > > > >> > wrote: > > > > >> > > > > > >> > > Hi Sean, > > > > >> > > > > > > >> > > When I tried to build the complete ctakes suite, i get build > > > failure > > > > >> for > > > > >> > > ctakes-ytex module with the following error: > > > > >> > > > > > > >> > > [ERROR] Failed to execute goal > > > > >> > > org.apache.maven.plugins:maven-antrun-plugin:3.1.0:run > > > > >> > > (generate-test-config) on project ctakes-ytex: An Ant > > > BuildException > > > > >> has > > > > >> > > occured: The following error occurred while executing this > line: > > > > >> > > [ERROR] > > > > >> > > > > > > >> > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\build-setup.xml:149: > > > > >> > The > > > > >> > > following error occurred while executing this line: > > > > >> > > [ERROR] > > > > >> > > > > > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:148: > > > > >> > The > > > > >> > > following error occurred while executing this line: > > > > >> > > [ERROR] > > > > >> > > > > > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:295: > > > > >> > The > > > > >> > > following error occurred while executing this line: > > > > >> > > [ERROR] > > > > >> > > > > > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: > > > > >> > Java > > > > >> > > returned: 1 > > > > >> > > [ERROR] around Ant part ...<ant antfile="build-setup.xml" > > > > >> dir="scripts" > > > > >> > > target="test.setup">... @ 5:70 in > > > > >> > > > > > > >> > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\target\antrun\build-main.xml > > > > >> > > > > > > >> > > Is this expected Sean? > > > > >> > > > > > > >> > > On Fri, 26 Apr 2024 at 21:30, Finan, Sean > > > > >> > > <sean.fi...@childrens.harvard.edu.invalid> wrote: > > > > >> > > > > > > >> > > > Hi all, > > > > >> > > > > > > > >> > > > There is a candidate for version 5.1.0 of Apache cTAKES > source > > > > code > > > > >> in > > > > >> > a > > > > >> > > > staging repository: > > > > >> > > > > > > > >> > > > > > > > >> > > > > > > >> > > > > > >> > > > > > > > > > > https://urldefense.com/v3/__https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/__;!!NZvER7FxgEiBAiR_!tcpxrhYwLK6D8VsrsLy0QyKhpcQbTXjfsU28PkcylePWmW2nvwu2u_5W3ISRgmXffKQuERIdgo__Owtxkd2ysxNkgAWbqNXsKw$ > > > > >> > > > > > > > >> > > > The code is contained within the file: > > > > >> > > > ctakes-5.1.0-source-release.zip< > > > > >> > > > > > > > >> > > > > > > >> > > > > > >> > > > > > > > > > > https://urldefense.com/v3/__https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip__;!!NZvER7FxgEiBAiR_!tcpxrhYwLK6D8VsrsLy0QyKhpcQbTXjfsU28PkcylePWmW2nvwu2u_5W3ISRgmXffKQuERIdgo__Owtxkd2ysxNkgAUTMj5tmQ$ > > > > >> > > > > > > > > >> > > > > > > > >> > > > I welcome you all to test your favorite pipeline(s) and > report > > > any > > > > >> > > issues. > > > > >> > > > I am calling a vote from the PMC to finish by 12:nn Eastern > > > time, > > > > >> next > > > > >> > > > Wednesday May 1. Please report any issues before that time. > > If > > > > any > > > > >> > > > 'road-block' issues are found they will need to be addressed > > > > before > > > > >> a > > > > >> > > > release. > > > > >> > > > > > > > >> > > > Thank you, > > > > >> > > > Sean > > > > >> > > > > > > > >> > > > > > > > >> > > > p.s. > > > > >> > > > > > > > >> > > > The 5.1.0 candidate is based upon the source code in the > > > > >> ctakes-5.1.0 > > > > >> > > tag: > > > > >> > > > > https://urldefense.com/v3/__https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0__;!!NZvER7FxgEiBAiR_!tcpxrhYwLK6D8VsrsLy0QyKhpcQbTXjfsU28PkcylePWmW2nvwu2u_5W3ISRgmXffKQuERIdgo__Owtxkd2ysxNkgAWWnLEmOA$ > > > > >> > > > > > > > >> > > > The ctakes-5.1.0 tag was made from the 5.1.0 branch: > > > > >> > > > > https://urldefense.com/v3/__https://github.com/apache/ctakes/tree/5.1.0__;!!NZvER7FxgEiBAiR_!tcpxrhYwLK6D8VsrsLy0QyKhpcQbTXjfsU28PkcylePWmW2nvwu2u_5W3ISRgmXffKQuERIdgo__Owtxkd2ysxNkgAVPu1xUow$ > > > > >> > > > > > > > >> > > > The 5.1.0 branch is a copy of the main branch: > > > > >> > > > > https://urldefense.com/v3/__https://github.com/apache/ctakes/tree/main__;!!NZvER7FxgEiBAiR_!tcpxrhYwLK6D8VsrsLy0QyKhpcQbTXjfsU28PkcylePWmW2nvwu2u_5W3ISRgmXffKQuERIdgo__Owtxkd2ysxNkgAU4h58rOQ$ > > > > >> > > > The version number in the 5.1.0 branch is different, but > there > > > are > > > > >> no > > > > >> > > code > > > > >> > > > differences between the two branches. > > > > >> > > > > > > > >> > > > > > > > >> > > > > > > > >> > > > > > > >> > > -- > > > > >> > > Regards, > > > > >> > > Gandhi > > > > >> > > > > > > >> > > "The best way to find urself is to lose urself in the service > of > > > > >> others > > > > >> > > !!!" > > > > >> > > > > > > >> > > > > > >> > > > > >> > > > > >> -- > > > > >> Regards, > > > > >> Gandhi > > > > >> > > > > >> "The best way to find urself is to lose urself in the service of > > > others > > > > >> !!!" > > > > >> > > > > > > > > > > > > > > > > > > -- > > > Regards, > > > Gandhi > > > > > > "The best way to find urself is to lose urself in the service of others > > > !!!" > > > > > > > > -- > Regards, > Gandhi > > "The best way to find urself is to lose urself in the service of others > !!!" > -- Regards, Gandhi "The best way to find urself is to lose urself in the service of others !!!"
